FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: G5ZL1

Calculation Name: 2W01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W01

Chain ID: A

ChEMBL ID:

UniProt ID: P72951

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091584.89946
FMO2-HF: Nuclear repulsion 2016184.919877
FMO2-HF: Total energy -75399.979582
FMO2-MP2: Total energy -75619.563328


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:435:MET)


Summations of interaction energy for fragment #1(A:435:MET)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-24.403-40.85352.666-14.775-21.4450.027
Interaction energy analysis for fragmet #1(A:435:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.063
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A437GLY0-0.041-0.0262.421-0.7702.0140.325-1.233-1.877-0.002
4A438ASP-1-0.850-0.9142.960-6.820-4.7290.137-0.816-1.411-0.006
5A439ARG10.8800.9474.5531.0601.220-0.001-0.008-0.1520.000
6A440ARG10.8520.9122.3812.2342.2492.085-0.489-1.612-0.003
7A441PRO00.0080.0208.3460.3220.3220.0000.0000.0000.000
8A442ILE0-0.017-0.0017.638-0.011-0.0110.0000.0000.0000.000
9A443THR00.019-0.00910.729-0.079-0.0790.0000.0000.0000.000
10A444ILE0-0.072-0.04012.4840.0940.0940.0000.0000.0000.000
11A445LEU00.0330.02314.801-0.107-0.1070.0000.0000.0000.000
12A446THR0-0.026-0.01117.0420.0980.0980.0000.0000.0000.000
13A447SER00.0440.01219.532-0.045-0.0450.0000.0000.0000.000
14A448ASP-1-0.834-0.90222.6570.3710.3710.0000.0000.0000.000
15A449LEU0-0.0170.00225.243-0.027-0.0270.0000.0000.0000.000
16A450ARG10.7490.84127.191-0.313-0.3130.0000.0000.0000.000
17A451GLY00.0080.00931.064-0.015-0.0150.0000.0000.0000.000
18A452PHE00.0400.01930.029-0.017-0.0170.0000.0000.0000.000
19A453THR00.005-0.00829.347-0.002-0.0020.0000.0000.0000.000
20A454SER0-0.043-0.01631.658-0.005-0.0050.0000.0000.0000.000
21A455THR0-0.010-0.01635.318-0.002-0.0020.0000.0000.0000.000
22A456SER0-0.0220.00232.959-0.007-0.0070.0000.0000.0000.000
23A457GLU-1-0.925-0.96534.8950.2130.2130.0000.0000.0000.000
24A458GLY0-0.103-0.04236.996-0.009-0.0090.0000.0000.0000.000
25A459LEU0-0.054-0.01335.200-0.009-0.0090.0000.0000.0000.000
26A460ASN0-0.016-0.02537.7660.0090.0090.0000.0000.0000.000
27A461PRO00.034-0.00734.0430.0060.0060.0000.0000.0000.000
28A462GLU-1-0.965-0.98433.1670.1660.1660.0000.0000.0000.000
29A463GLU-1-0.864-0.92333.9040.1570.1570.0000.0000.0000.000
30A464VAL00.0160.01530.4650.0060.0060.0000.0000.0000.000
31A465VAL00.0120.00228.3620.0130.0130.0000.0000.0000.000
32A466LYS10.9160.96929.228-0.151-0.1510.0000.0000.0000.000
33A467VAL00.0350.01230.9810.0010.0010.0000.0000.0000.000
34A468LEU00.0280.01826.3320.0050.0050.0000.0000.0000.000
35A469ASN0-0.037-0.01925.9070.0380.0380.0000.0000.0000.000
36A470ILE0-0.044-0.01226.8310.0030.0030.0000.0000.0000.000
37A471TYR00.0580.01924.647-0.002-0.0020.0000.0000.0000.000
38A472PHE0-0.016-0.01822.4880.0110.0110.0000.0000.0000.000
39A473GLY0-0.020-0.00423.0420.0190.0190.0000.0000.0000.000
40A474LYS10.8760.94824.570-0.187-0.1870.0000.0000.0000.000
41A475MET0-0.007-0.00922.413-0.004-0.0040.0000.0000.0000.000
42A476ALA0-0.010-0.00720.0320.0180.0180.0000.0000.0000.000
43A477ASP-1-0.875-0.91020.1350.2130.2130.0000.0000.0000.000
44A478VAL0-0.014-0.00421.699-0.010-0.0100.0000.0000.0000.000
45A479ILE00.022-0.00616.206-0.002-0.0020.0000.0000.0000.000
46A480THR0-0.061-0.03516.7000.0170.0170.0000.0000.0000.000
47A481HIS0-0.131-0.05717.442-0.051-0.0510.0000.0000.0000.000
48A482HIS0-0.023-0.02317.988-0.035-0.0350.0000.0000.0000.000
49A483GLY0-0.0020.00314.298-0.010-0.0100.0000.0000.0000.000
50A484GLY0-0.021-0.00812.5010.0230.0230.0000.0000.0000.000
51A485THR0-0.059-0.0628.588-0.128-0.1280.0000.0000.0000.000
52A486ILE00.0200.00611.7600.0800.0800.0000.0000.0000.000
53A487ASP-1-0.824-0.8999.1872.3252.3250.0000.0000.0000.000
54A488GLU-1-0.906-0.96511.7771.2411.2410.0000.0000.0000.000
55A489PHE00.0360.03614.825-0.055-0.0550.0000.0000.0000.000
56A490MET0-0.094-0.00517.8070.0450.0450.0000.0000.0000.000
57A491GLY00.0130.00320.264-0.030-0.0300.0000.0000.0000.000
58A492ASP-1-0.823-0.92423.8850.3380.3380.0000.0000.0000.000
59A493GLY00.0600.02722.050-0.022-0.0220.0000.0000.0000.000
60A494ILE0-0.059-0.02717.7120.0290.0290.0000.0000.0000.000
61A495LEU0-0.042-0.01013.055-0.015-0.0150.0000.0000.0000.000
62A496VAL00.018-0.01313.8610.0760.0760.0000.0000.0000.000
63A497LEU0-0.064-0.0308.0160.0550.0550.0000.0000.0000.000
64A498PHE00.0520.03410.947-0.028-0.0280.0000.0000.0000.000
65A499GLY00.0900.0388.163-0.020-0.0200.0000.0000.0000.000
66A500ALA0-0.0270.0004.633-0.389-0.268-0.001-0.023-0.0970.000
67A501PRO00.0350.0243.488-0.5660.0570.089-0.181-0.5310.000
68A502THR00.0030.0042.841-5.271-3.7220.267-0.897-0.920-0.012
69A503SER0-0.035-0.0085.6510.2760.2760.0000.0000.0000.000
70A504GLN0-0.085-0.0517.965-0.115-0.1150.0000.0000.0000.000
71A505GLN0-0.014-0.01911.7010.0530.0530.0000.0000.0000.000
72A506ASP-1-0.801-0.88814.822-0.009-0.0090.0000.0000.0000.000
73A507ASP-1-0.742-0.86510.4030.0760.0760.0000.0000.0000.000
74A508ALA00.0330.01013.8330.0630.0630.0000.0000.0000.000
75A509LEU00.005-0.01016.7090.0210.0210.0000.0000.0000.000
76A510ARG10.7660.88611.858-0.123-0.1230.0000.0000.0000.000
77A511ALA0-0.0070.00915.9050.0260.0260.0000.0000.0000.000
78A512VAL0-0.002-0.00917.7170.0140.0140.0000.0000.0000.000
79A513ALA0-0.022-0.00221.0670.0020.0020.0000.0000.0000.000
80A514CYS00.0130.02318.9480.0120.0120.0000.0000.0000.000
81A515GLY00.0430.01220.9880.0070.0070.0000.0000.0000.000
82A516VAL0-0.020-0.02422.840-0.005-0.0050.0000.0000.0000.000
83A517GLU-1-0.782-0.87424.0490.1530.1530.0000.0000.0000.000
84A518MET0-0.024-0.02420.8940.0060.0060.0000.0000.0000.000
85A519GLN00.022-0.01025.211-0.013-0.0130.0000.0000.0000.000
86A520LEU0-0.084-0.03628.424-0.012-0.0120.0000.0000.0000.000
87A521ALA00.0150.00427.274-0.011-0.0110.0000.0000.0000.000
88A522LEU00.0230.01629.196-0.001-0.0010.0000.0000.0000.000
89A523ARG10.8690.92330.800-0.140-0.1400.0000.0000.0000.000
90A524GLU-1-0.887-0.94231.3720.1400.1400.0000.0000.0000.000
91A525VAL00.0230.00929.435-0.004-0.0040.0000.0000.0000.000
92A526ASN00.0070.00432.8430.0030.0030.0000.0000.0000.000
93A527GLN0-0.0290.00335.639-0.010-0.0100.0000.0000.0000.000
94A528GLN0-0.023-0.01633.3420.0010.0010.0000.0000.0000.000
95A529VAL00.007-0.00333.474-0.003-0.0030.0000.0000.0000.000
96A530THR00.010-0.00536.622-0.004-0.0040.0000.0000.0000.000
97A531GLY0-0.064-0.02140.056-0.006-0.0060.0000.0000.0000.000
98A532LEU0-0.087-0.04435.930-0.004-0.0040.0000.0000.0000.000
99A533GLY0-0.025-0.00640.2330.0000.0000.0000.0000.0000.000
100A534LEU0-0.039-0.00837.6060.0000.0000.0000.0000.0000.000
101A535GLN0-0.024-0.01739.239-0.005-0.0050.0000.0000.0000.000
102A536PRO0-0.021-0.01136.5680.0080.0080.0000.0000.0000.000
103A537LEU0-0.0010.00330.2170.0040.0040.0000.0000.0000.000
104A538GLU-1-0.891-0.95032.7400.1780.1780.0000.0000.0000.000
105A539MET0-0.012-0.00424.4190.0070.0070.0000.0000.0000.000
106A540GLY00.0180.01127.807-0.022-0.0220.0000.0000.0000.000
107A541ILE00.019-0.01022.1960.0350.0350.0000.0000.0000.000
108A542GLY0-0.025-0.00322.670-0.038-0.0380.0000.0000.0000.000
109A543ILE0-0.005-0.00718.1810.0490.0490.0000.0000.0000.000
110A544ASN0-0.057-0.03717.977-0.103-0.1030.0000.0000.0000.000
111A545THR00.0470.04714.6120.0660.0660.0000.0000.0000.000
112A546GLY0-0.016-0.00614.157-0.065-0.0650.0000.0000.0000.000
113A547GLU-1-0.896-0.95511.6410.0600.0600.0000.0000.0000.000
114A548VAL0-0.055-0.0298.8730.0400.0400.0000.0000.0000.000
115A549VAL0-0.028-0.0146.312-0.196-0.1960.0000.0000.0000.000
116A550VAL00.0400.0213.431-0.3580.2060.585-0.240-0.9090.000
117A551GLY00.017-0.0262.010-0.875-3.47911.659-6.463-2.5920.010
118A552ASN0-0.059-0.0451.900-7.950-25.13323.1120.348-6.2770.019
119A553ILE00.0130.0213.610-1.744-1.8010.0770.240-0.2600.004
120A554GLY00.0190.0107.361-0.442-0.4420.0000.0000.0000.000
121A555SER0-0.040-0.01310.202-0.120-0.1200.0000.0000.0000.000
122A556GLU-1-0.816-0.90410.8110.5020.5020.0000.0000.0000.000
123A557LYS10.8240.89712.080-0.323-0.3230.0000.0000.0000.000
124A558ARG10.9750.97412.428-0.867-0.8670.0000.0000.0000.000
125A559THR0-0.0300.0056.9980.2050.2050.0000.0000.0000.000
126A560LYS10.7890.8527.605-2.110-2.1100.0000.0000.0000.000
127A561TYR0-0.011-0.0162.152-3.590-8.10314.332-5.013-4.8070.017
128A562GLY00.0510.0235.706-0.752-0.7520.0000.0000.0000.000
129A563VAL00.0480.0166.4220.7580.7580.0000.0000.0000.000
130A564VAL0-0.031-0.0078.954-0.397-0.3970.0000.0000.0000.000
131A565GLY00.0370.00310.899-0.080-0.0800.0000.0000.0000.000
132A566ALA0-0.008-0.01313.6920.0040.0040.0000.0000.0000.000
133A567GLN00.0570.03014.860-0.033-0.0330.0000.0000.0000.000
134A568VAL00.0720.04312.342-0.054-0.0540.0000.0000.0000.000
135A569ASN0-0.013-0.01415.490-0.015-0.0150.0000.0000.0000.000
136A570LEU0-0.023-0.00218.806-0.053-0.0530.0000.0000.0000.000
137A571THR00.0080.00416.751-0.049-0.0490.0000.0000.0000.000
138A572TYR00.0800.00016.612-0.030-0.0300.0000.0000.0000.000
139A573ARG10.8830.94621.559-0.506-0.5060.0000.0000.0000.000
140A574ILE0-0.0280.01122.088-0.035-0.0350.0000.0000.0000.000
141A575GLU-1-0.772-0.88923.0510.3200.3200.0000.0000.0000.000
142A576SER0-0.063-0.04525.056-0.030-0.0300.0000.0000.0000.000
143A577TYR0-0.056-0.04527.714-0.027-0.0270.0000.0000.0000.000
144A578THR0-0.0690.02327.568-0.031-0.0310.0000.0000.0000.000
145A579THR0-0.014-0.01430.2670.0020.0020.0000.0000.0000.000
146A580GLY00.0830.02931.5470.0100.0100.0000.0000.0000.000
147A581GLY0-0.047-0.01331.365-0.014-0.0140.0000.0000.0000.000
148A582GLN0-0.0150.00730.371-0.004-0.0040.0000.0000.0000.000
149A583ILE00.0130.00124.3040.0240.0240.0000.0000.0000.000
150A584PHE0-0.0120.00626.225-0.025-0.0250.0000.0000.0000.000
151A585ILE00.0220.00922.4230.0360.0360.0000.0000.0000.000
152A586SER00.0430.00820.604-0.031-0.0310.0000.0000.0000.000
153A587SER00.0480.00423.240-0.006-0.0060.0000.0000.0000.000
154A588THR00.0120.00519.030-0.016-0.0160.0000.0000.0000.000
155A589THR00.0090.01418.690-0.003-0.0030.0000.0000.0000.000
156A590LEU00.0110.01020.046-0.018-0.0180.0000.0000.0000.000
157A591GLU-1-0.974-0.98622.2770.0430.0430.0000.0000.0000.000
158A592ALA0-0.082-0.02817.292-0.025-0.0250.0000.0000.0000.000
159A593ALA0-0.004-0.00119.342-0.022-0.0220.0000.0000.0000.000
160A594GLY0-0.002-0.00220.666-0.022-0.0220.0000.0000.0000.000
161A595ASP-1-0.856-0.93823.9820.0250.0250.0000.0000.0000.000
162A596ARG10.8520.93523.302-0.004-0.0040.0000.0000.0000.000
163A597VAL00.0020.01523.1890.0110.0110.0000.0000.0000.000
164A598HIS0-0.029-0.01226.383-0.010-0.0100.0000.0000.0000.000
165A599VAL00.005-0.00728.3910.0140.0140.0000.0000.0000.000
166A600ASN0-0.013-0.01330.996-0.019-0.0190.0000.0000.0000.000
167A601GLY0-0.017-0.01032.671-0.008-0.0080.0000.0000.0000.000
168A602ASN0-0.057-0.02331.3630.0130.0130.0000.0000.0000.000
169A603ARG10.9740.99931.605-0.173-0.1730.0000.0000.0000.000
170A604THR00.0000.00731.4030.0110.0110.0000.0000.0000.000
171A605VAL0-0.020-0.00628.876-0.003-0.0030.0000.0000.0000.000
172A606GLN00.016-0.00329.684-0.009-0.0090.0000.0000.0000.000
173A607PRO0-0.0070.02326.137-0.004-0.0040.0000.0000.0000.000
174A608LYS10.9730.96228.673-0.237-0.2370.0000.0000.0000.000
175A609GLY00.0130.00827.1890.0210.0210.0000.0000.0000.000
176A610VAL0-0.0250.00424.9270.0140.0140.0000.0000.0000.000
177A611LYS10.7820.89225.132-0.207-0.2070.0000.0000.0000.000
178A612ASP-1-0.768-0.88128.2830.1310.1310.0000.0000.0000.000
179A613PRO0-0.014-0.01728.9280.0180.0180.0000.0000.0000.000
180A614VAL0-0.035-0.01325.164-0.003-0.0030.0000.0000.0000.000
181A615VAL00.0130.00628.3270.0000.0000.0000.0000.0000.000
182A616ILE0-0.081-0.03625.9910.0130.0130.0000.0000.0000.000
183A617TRP0-0.012-0.04126.114-0.026-0.0260.0000.0000.0000.000
184A618ASP-1-0.803-0.88727.6440.1750.1750.0000.0000.0000.000
185A619VAL0-0.015-0.01325.194-0.016-0.0160.0000.0000.0000.000
186A620ALA0-0.0010.00728.6570.0040.0040.0000.0000.0000.000
187A621GLY00.043-0.00428.8420.0020.0020.0000.0000.0000.000
188A622VAL0-0.073-0.01824.0480.0020.0020.0000.0000.0000.000
189A623GLY00.0680.04127.299-0.003-0.0030.0000.0000.0000.000
190A624GLU-1-0.860-0.91727.6090.0180.0180.0000.0000.0000.000
191A625PRO0-0.076-0.04724.517-0.003-0.0030.0000.0000.0000.000
192A626TYR0-0.008-0.02719.9840.0000.0000.0000.0000.0000.000
193A627ASN0-0.064-0.04826.7350.0050.0050.0000.0000.0000.000
194A628LEU0-0.0150.02025.2660.0030.0030.0000.0000.0000.000
195A629SER00.015-0.02429.3450.0040.0040.0000.0000.0000.000
196A630LEU00.0150.01729.0800.0030.0030.0000.0000.0000.000
197A631ALA0-0.0070.00732.5330.0000.0000.0000.0000.0000.000
198A632VAL0-0.026-0.01435.666-0.002-0.0020.0000.0000.0000.000
199A633GLU-1-0.900-0.94535.6590.0540.0540.0000.0000.0000.000
200A634GLU-1-1.003-0.99638.9210.0600.0600.0000.0000.0000.000
201A635GLN0-0.047-0.01940.197-0.007-0.0070.0000.0000.0000.000